New syndromic combined immunodeficiency with severe neurodevelopmental defects caused by biallelic null variants in the PPM1D gene

PPM1D (protein phosphatase Mn2+/Mg2+-dependent 1D) is a phosphatase that targets proteins related to the DNA damage repair system. C-terminal variants in PPM1D have been associated with: i) malignancy as somatic variants; and ii) Jansen-de-Vries (JdV) syndrome as germline heterozygous variants. JdV syndrome curses with moderate neurodevelopmental alterations and behavioral problems, such as autistic spectrum disorders (ASD), without reports of immunodeficiency. We describe two siblings (9 and 11 years old) born to consanguineous parents with progressive B and NK cell lymphopenia, agammaglobulinemia, non-ulcerative colitis and severe neurodevelopmental defects including microcephaly, severe encephalopathy, profound cognitive deficiency, and refractory epilepsy. Exome analysis revealed a homozygous N-terminal truncating variant in PPM1D (p.Thr174fs*6) in the two siblings inherited from their healthy heterozygous parents. The siblings’ clinical phenotype was markedly more severe than in the reported JdV patients, suggesting a different mechanism of action. To test this, we included a pediatric patient with classical JdV syndrome carrying an heterozygous PPM1D variant (p. Ser403fs*30). Using primary cells and exogenous overexpression we showed that mutation p.T174fs*6 abrogated protein expression by increased proteasome degradation, leading to no protein expression in a homozygous patient and a reduction in a haplosufficient parent. In contrast, the JdV variant (p.Ser403fs*30) led to accumulation of the truncated protein with conserved phosphatase activity, resulting in a previously undescribed gain-of-function (GOF) mechanism. We also demonstrated that chemical inhibition of WT-PPM1D in-vitro dramatically decreased B cell viability. This data, similar to the reported B cell deficiency in PPM1D-KO mice, helps to address the humoral deficiency in the patients, while not observed in the heterozygous parents nor JdV patient. To further explore NK cell deficiency, we will evaluate PPM1D-KO mice. We have generated EBV-B cell-derived iPSCs from PPM1D-null, PPM1D-haplosufficient an GOF-JdV individuals, to generate artificial cerebral organoids that will allow us to explore PPM1D gene-dosage effect in neurodevelopment and its potential manipulation. Here we report a novel biallelic PPM1D-null deficiency impairing B cell development. Besides, PPM1D dysregulation either by no protein expression or GOF appears to cause neurodevelopment abnormalities. Future studies will